Next Generation Dx Summit

Dinner Short Course 11

NGS for Infectious Disease Diagnostics

Wednesday, August 20 | 6:30pm - 8:30pm

 

Next-generation sequencing technology is increasingly being used in the detection of known, uncommon, or novel pathogens with emerging clinical applications including outbreak investigation and infectious disease diagnosis. This course will discuss the applications of this technology and some of the current challenges being faced.

The course will cover:

1. Clinical laboratory implementation of an unbiased NGS assay for pathogen detection

Erik Samayoa, Clinical Lab Scientist, UCSF Viral Diagnostics and Discovery Center

  • Workflow overview
  • Infrastructure needed for assay implementation
  • Control implementation for monitoring assay performance
  • Assay sensitivity across sample types (e.g. blood, bronchoalveolar lavage, cerebrospinal fluid)
  • Regulatory and quality control challenges

2. From sequence-to-answer: bioinformatics analysis of NGS data in infectious diseases

Samia Naccache, Ph.D., Associate Specialist, Laboratory Medicine, UCSF

  • Bioinformatics pipeline (SURPI) for pathogen detection: construction and validation
  • Results reporting and interpretation for the end-user
  • Challenges in interpretation (user interface, signal noise)
  • Clinical case reports of unbiased NGS for infectious disease diagnosis

3. Other applications of NGS in infectious diseases

Samia Naccache, Ph.D., Associate Specialist, Laboratory Medicine, UCSF

Erik Samayoa, Clinical Lab Scientist, UCSF Viral Diagnostics and Discovery Center

  • 16S/18S amplicon sequencing
  • Whole-genome sequencing of bacteria and viruses
  • Microbiome analysis
  • Pathogen enrichment panels for detection and quasispecies analysis
  • Host transcriptome sequencing for biomarker identification

Instructors:

Samia Naccache, Ph.D., Associate Specialist, Laboratory Medicine, UCSF 

SamiaNaccacheSamia Naccache earned her Ph.D. from UCSD in cell biology with a research focus on molecular motors in vesicle trafficking. After completing a postdoctoral fellowship in adenovirus innate immunity, she joined the Chiu laboratory and the UCSF-Abbott Viral Diagnostics and Discovery Center. In collaboration with the CLIA-certified UCSF clinical microbiology laboratory, she has been involved in the validation of microarray-based diagnostic platforms, pathogen discovery, and bioinformatics pipeline development for NGS.

 

Erik Samayoa, Clinical Lab Scientist, UCSF Viral Diagnostics and Discovery Center 

ErikSamayoaErik Samayoa is currently a research clinical laboratory scientist at the UCSF-Abbott Viral Diagnostics and Discovery Center. One of the priorities of the center is the development of rapid NGS-based clinical diagnostics for pathogen detection. Erik has been developing and validating protocols for unbiased NGS-based pathogen detection in the clinical laboratory. He has 12 years of prior clinical and research experience at UCSF including work in clinical chemistry, prions, and molecular diagnostics.



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